Site homepage 404 Page not Found

I'm developing a website with some medium-level customisation, with out-of-the-box modules included. At some point in the development stage the homepage has gone AWOL. I am getting a 404 Page Not Found error page when I try to visit the root directory and /home pages.

Now it gets weird.

If I append /?flush (with or without the =1 or =all variable) the homepage works. If I empty the silverstripe-cache folder, it works once. If I delete /index.php file it works once, then it breaks. If I upload the /index.php file it works once, then it breaks.

I have tried shifting to a different host, database repairs, moving directories, dropping a fresh install on top all without luck. Any tips would be extremely well received.